Variant report

Variant	rs13407966
Chromosome Location	chr2:54514538-54514539
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54511470..54513165-chr2:54513322..54515700,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1001296	1.00[CHD][hapmap]
rs10191400	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10199945	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10207892	1.00[CHD][hapmap]
rs11125521	1.00[CHD][hapmap]
rs11891079	1.00[CHD][hapmap]
rs11896279	1.00[CHD][hapmap]
rs13400567	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13407896	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13407991	1.00[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13414565	1.00[CHD][hapmap]
rs13432937	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17045575	1.00[CHD][hapmap]
rs2090182	1.00[CHD][hapmap]
rs34126566	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59891234	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72901527	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72901533	0.90[EUR][1000 genomes]
rs72901551	0.80[EUR][1000 genomes]
rs72910615	0.98[EUR][1000 genomes]
rs72910625	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72910627	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72910631	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7568345	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7595149	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs964092	1.00[CEU][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv532512	chr2:54453210-54630755	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1004632	chr2:54469283-54590480	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv998172	chr2:54488511-54537474	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1011754	chr2:54494644-54533805	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv14065	chr2:54513051-54517656	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
12	esv3459572	chr2:54513069-54517863	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
13	esv3459573	chr2:54513117-54517838	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
14	esv3459575	chr2:54513215-54517733	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54449800-54535200	Weak transcription	Primary T cells from cord blood	blood
2	chr2:54483400-54521200	Weak transcription	Pancreas	Pancrea
3	chr2:54488200-54514600	Weak transcription	Aorta	Aorta
4	chr2:54500200-54517800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr2:54501600-54537600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:54502600-54514600	Weak transcription	HSMMtube	muscle
7	chr2:54506800-54514600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:54507600-54514800	Weak transcription	Brain Angular Gyrus	brain
9	chr2:54510400-54514600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:54513000-54516400	Weak transcription	Primary B cells from cord blood	blood
11	chr2:54513600-54514600	Weak transcription	Brain Substantia Nigra	brain
12	chr2:54513600-54515800	Weak transcription	HepG2	liver
13	chr2:54514200-54515000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:54514200-54515200	Enhancers	Adipose Nuclei	Adipose
15	chr2:54514200-54515200	Enhancers	Psoas Muscle	Psoas
16	chr2:54514200-54516000	Enhancers	Fetal Muscle Leg	muscle
17	chr2:54514200-54516000	Enhancers	Rectal Smooth Muscle	rectum
18	chr2:54514200-54516000	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:54514400-54515400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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